Evaluating performance of biomedical image retrieval systems - an overview of the medical image retrieval task at ImageCLEF 2004-2013

Medical image retrieval and classification have been extremely active research topics over the past 15 years. Within the ImageCLEF benchmark in medical image retrieval and classification, a standard test bed was created that allows researchers to compare their approaches and ideas on increasingly large and varied data sets including generated ground truth. This article describes the lessons learned in ten evaluation campaigns. A detailed analysis of the data also highlights the value of the resources created

Experiences from the ImageCLEF Medical Retrieval and Annotation Tasks

The medical tasks in ImageCLEF have been run every year from 2004-2018 and many different tasks and data sets have been used over these years. The created resources are being used by many researchers well beyond the actual evaluation campaigns and are allowing to compare the performance of many techniques on the same grounds and in a reproducible way. Many of the larger data sets are from the medical literature, as such images are easier to obtain and to share than clinical data, which was used in a few smaller ImageCLEF challenges that are specifically marked with the disease type and anatomic region. This chapter describes the main results of the various tasks over the years, including data, participants, types of tasks evaluated and also the lessons learned in organizing such tasks for the scientific community

Use Case Oriented Medical Visual Information Retrieval & System Evaluation

Large amounts of medical visual data are produced daily in hospitals, while new imaging techniques continue to emerge. In addition, many images are made available continuously via publications in the scientific literature and can also be valuable for clinical routine, research and education. Information retrieval systems are useful tools to provide access to the biomedical literature and fulfil the information needs of medical professionals. The tools developed in this thesis can potentially help clinicians make decisions about difficult diagnoses via a case-based retrieval system based on a use case associated with a specific evaluation task. This system retrieves articles from the biomedical literature when querying with a case description and attached images. This thesis proposes a multimodal approach for medical case-based retrieval with focus on the integration of visual information connected to text. Furthermore, the ImageCLEFmed evaluation campaign was organised during this thesis promoting medical retrieval system evaluation

Fusion Techniques in Biomedical Information Retrieval

For difficult cases clinicians usually use their experience and also the information found in textbooks to determine a diagnosis. Computer tools can help them supply the relevant information now that much medical knowledge is available in digital form. A biomedical search system such as developed in the Khresmoi project (that this chapter partially reuses) has the goal to fulfil information needs of physicians. This chapter concentrates on information needs for medical cases that contain a large variety of data, from free text, structured data to images. Fusion techniques will be compared to combine the various information sources to supply cases similar to an example case given. This can supply physicians with answers to problems similar to the one they are analyzing and can help in diagnosis and treatment planning

Overview of the ImageCLEF 2013 medical tasks

In 2013, the tenth edition of the medical task of the Image-CLEF benchmark was organized. For the first time, the ImageCLEFmedworkshop takes place in the United States of America at the annualAMIA (American Medical Informatics Association) meeting even thoughthe task was organized as in previous years in connection with the otherImageCLEF tasks. Like 2012, a subset of the open access collection ofPubMed Central was distributed. This year, there were four subtasks:modality classification, compound figure separation, image–based andcase–based retrieval. The compound figure separation task was includeddue to the large number of multipanel images available in the literatureand the importance to separate them for targeted retrieval. More com-pound figures were also included in the modality classification task tomake it correspond to the distribution in the full database. The retrievaltasks remained in the same format as in previous years but a largernumber of tasks were available for image–based and case–based tasks.This paper presents an analysis of the techniques applied by the tengroups participating 2013 in ImageCLEFmed

Comparing Fusion Techniques for the ImageCLEF 2013 Medical Case Retrieval Task

Retrieval systems can supply similar cases with a proven diagnosis to a new example case under observation to help clinicians during their work. The ImageCLEFmed evaluation campaign proposes a framework where research groups can compare case-based retrieval approaches. This paper focuses on the case-based task and adds results of the compound figure separation and modality classification tasks. Several fusion approaches are compared to identify the approaches best adapted to the heterogeneous data of the task. Fusion of visual and textual features is analyzed, demonstrating that the selection of the fusion strategy can improve the best performance on the case-based retrieval task

ImageCLEF 2013: The vision, the data and the open challenges

This paper presents an overview of the ImageCLEF 2013 lab. Since its first edition in 2003, ImageCLEF has become one of the key initiatives promoting the benchmark evaluation of algorithms for the cross-language annotation and retrieval of images in various domains, such as public and personal images, to data acquired by mobile robot platforms and botanic collections. Over the years, by providing new data collections and challenging tasks to the community of interest, the ImageCLEF lab has achieved an unique position in the multi lingual image annotation and retrieval research landscape. The 2013 edition consisted of three tasks: the photo annotation and retrieval task, the plant identification task and the robot vision task. Furthermore, the medical annotation task, that traditionally has been under the ImageCLEF umbrella and that this year celebrates its tenth anniversary, has been organized in conjunction with AMIA for the first time. The paper describes the tasks and the 2013 competition, giving an unifying perspective of the present activities of the lab while discussion the future challenges and opportunities.This work has been partially supported by the Halser Foundation (B. C.),by the LiMoSINe FP7 project under grant # 288024 (B. T.), by the Khresmoi (grant# 257528) and PROMISE ( grant # 258191) FP 7 projects (H.M.) and by the tranScriptorium FP7 project under grant # 600707 (M. V., R. P.)Caputo ., B.; Muller ., H.; Thomee ., B.; Villegas, M.; Paredes Palacios, R.; Zellhofer ., D.; Goeau ., H.... (2013). ImageCLEF 2013: The vision, the data and the open challenges. En Information Access Evaluation. Multilinguality, Multimodality, and Visualization. Springer Verlag (Germany). 8138:250-268. https://doi.org/10.1007/978-3-642-40802-1_26S2502688138Muller, H., Clough, P., Deselaers, T., Caputo, B.: ImageCLEF: experimental evaluation in visual information retrieval. Springer (2010)Tsikrika, T., Seco de Herrera, A.G., Müller, H.: Assessing the scholarly impact of imageCLEF. In: Forner, P., Gonzalo, J., Kekäläinen, J., Lalmas, M., de Rijke, M. (eds.) CLEF 2011. LNCS, vol. 6941, pp. 95–106. Springer, Heidelberg (2011)Huiskes, M., Lew, M.: The MIR Flickr retrieval evaluation. In: Proceedings of the 10th ACM Conference on Multimedia Information Retrieval, Vancouver, BC, Canada, pp. 39–43 (2008)Huiskes, M., Thomee, B., Lew, M.: New trends and ideas in visual concept detection. In: Proceedings of the 11th ACM Conference on Multimedia Information Retrieval, Philadelphia, PA, USA, pp. 527–536 (2010)Villegas, M., Paredes, R.: Overview of the ImageCLEF 2012 Scalable Web Image Annotation Task. In: CLEF 2012 Evaluation Labs and Workshop, Online Working Notes, Rome, Italy (2012)Zellhöfer, D.: Overview of the Personal Photo Retrieval Pilot Task at ImageCLEF 2012. In: CLEF 2012 Evaluation Labs and Workshop, Online Working Notes, Rome, Italy (2012)Villegas, M., Paredes, R., Thomee, B.: Overview of the ImageCLEF 2013 Scalable Concept Image Annotation Subtask. In: CLEF 2013 Evaluation Labs and Workshop, Online Working Notes, Valencia, Spain (2013)Zellhöfer, D.: Overview of the ImageCLEF 2013 Personal Photo Retrieval Subtask. In: CLEF 2013 Evaluation Labs and Workshop, Online Working Notes, Valencia, Spain (2013)Leafsnap (2011)Plantnet (2013)Mobile flora (2013)Folia (2012)Goëau, H., Bonnet, P., Joly, A., Bakic, V., Boujemaa, N., Barthelemy, D., Molino, J.F.: The imageclef 2013 plant identification task. In: ImageCLEF 2013 Working Notes (2013)Pronobis, A., Xing, L., Caputo, B.: Overview of the CLEF 2009 robot vision track. In: Peters, C., Caputo, B., Gonzalo, J., Jones, G.J.F., Kalpathy-Cramer, J., Müller, H., Tsikrika, T. (eds.) CLEF 2009. LNCS, vol. 6242, pp. 110–119. Springer, Heidelberg (2010)Pronobis, A., Caputo, B.: The robot vision task. In: Muller, H., Clough, P., Deselaers, T., Caputo, B. (eds.) ImageCLEF. The Information Retrieval Series, vol. 32, pp. 185–198. Springer, Heidelberg (2010)Pronobis, A., Christensen, H.I., Caputo, B.: Overview of the imageCLEF@ICPR 2010 robot vision track. In: Ünay, D., Çataltepe, Z., Aksoy, S. (eds.) ICPR 2010. LNCS, vol. 6388, pp. 171–179. Springer, Heidelberg (2010)Martinez-Gomez, J., Garcia-Varea, I., Caputo, B.: Overview of the imageclef 2012 robot vision task. In: CLEF 2012 Working Notes (2012)Rusu, R., Cousins, S.: 3d is here: Point cloud library (pcl). In: 2011 IEEE International Conference on Robotics and Automation (ICRA), pp. 1–4. IEEE (2011)Bosch, A., Zisserman, A., Munoz, X.: Image classification using random forests and ferns. In: International Conference on Computer Vision, pp. 1–8. Citeseer (2007)Dalal, N., Triggs, B.: Histograms of oriented gradients for human detection. In: IEEE Computer Society Conference on Computer Vision and Pattern Recognition, CVPR 2005, vol. 1, pp. 886–893. IEEE (2005)Linde, O., Lindeberg, T.: Object recognition using composed receptive field histograms of higher dimensionality. In: Proc. ICPR. Citeseer (2004)Orabona, F., Castellini, C., Caputo, B., Luo, J., Sandini, G.: Indoor place recognition using online independent support vector machines. In: Proc. BMVC, vol. 7 (2007)Orabona, F., Castellini, C., Caputo, B., Jie, L., Sandini, G.: On-line independent support vector machines. Pattern Recognition 43, 1402–1412 (2010)Orabona, F., Jie, L., Caputo, B.: Online-Batch Strongly Convex Multi Kernel Learning. In: Proc. of Computer Vision and Pattern Recognition, CVPR (2010)Orabona, F., Jie, L., Caputo, B.: Multi kernel learning with online-batch optimization. Journal of Machine Learning Research 13, 165–191 (2012)Clough, P., Müller, H., Sanderson, M.: The CLEF 2004 cross-language image retrieval track. In: Peters, C., Clough, P., Gonzalo, J., Jones, G.J.F., Kluck, M., Magnini, B. (eds.) CLEF 2004. LNCS, vol. 3491, pp. 597–613. Springer, Heidelberg (2005)Clough, P., Müller, H., Deselaers, T., Grubinger, M., Lehmann, T.M., Jensen, J., Hersh, W.: The CLEF 2005 cross–language image retrieval track. In: Peters, C., Gey, F.C., Gonzalo, J., Müller, H., Jones, G.J.F., Kluck, M., Magnini, B., de Rijke, M., Giampiccolo, D. (eds.) CLEF 2005. LNCS, vol. 4022, pp. 535–557. Springer, Heidelberg (2006)Müller, H., Deselaers, T., Deserno, T., Clough, P., Kim, E., Hersh, W.: Overview of the imageCLEFmed 2006 medical retrieval and medical annotation tasks. In: Peters, C., Clough, P., Gey, F.C., Karlgren, J., Magnini, B., Oard, D.W., de Rijke, M., Stempfhuber, M. (eds.) CLEF 2006. LNCS, vol. 4730, pp. 595–608. Springer, Heidelberg (2007)Müller, H., Deselaers, T., Deserno, T., Kalpathy–Cramer, J., Kim, E., Hersh, W.: Overview of the imageCLEFmed 2007 medical retrieval and medical annotation tasks. In: Peters, C., Jijkoun, V., Mandl, T., Müller, H., Oard, D.W., Peñas, A., Petras, V., Santos, D. (eds.) CLEF 2007. LNCS, vol. 5152, pp. 472–491. Springer, Heidelberg (2008)Müller, H., Kalpathy–Cramer, J., Eggel, I., Bedrick, S., Radhouani, S., Bakke, B., Kahn Jr., C.E., Hersh, W.: Overview of the CLEF 2009 medical image retrieval track. In: Peters, C., Caputo, B., Gonzalo, J., Jones, G.J.F., Kalpathy-Cramer, J., Müller, H., Tsikrika, T. (eds.) CLEF 2009, Part II. LNCS, vol. 6242, pp. 72–84. Springer, Heidelberg (2010)Tommasi, T., Caputo, B., Welter, P., Güld, M.O., Deserno, T.M.: Overview of the CLEF 2009 medical image annotation track. In: Peters, C., Caputo, B., Gonzalo, J., Jones, G.J.F., Kalpathy-Cramer, J., Müller, H., Tsikrika, T. (eds.) CLEF 2009. LNCS, vol. 6242, pp. 85–93. Springer, Heidelberg (2010)Müller, H., Clough, P., Deselaers, T., Caputo, B. (eds.): ImageCLEF – Experimental Evaluation in Visual Information Retrieval. The Springer International Series on Information Retrieval, vol. 32. Springer, Heidelberg (2010)Kalpathy-Cramer, J., Müller, H., Bedrick, S., Eggel, I., García Seco de Herrera, A., Tsikrika, T.: The CLEF 2011 medical image retrieval and classification tasks. In: Working Notes of CLEF 2011 (Cross Language Evaluation Forum) (2011)Müller, H., García Seco de Herrera, A., Kalpathy-Cramer, J., Demner Fushman, D., Antani, S., Eggel, I.: Overview of the ImageCLEF 2012 medical image retrieval and classification tasks. In: Working Notes of CLEF 2012 (Cross Language Evaluation Forum) (2012)García Seco de Herrera, A., Kalpathy-Cramer, J., Demner Fushman, D., Antani, S., Müller, H.: Overview of the ImageCLEF 2013 medical tasks. In: Working Notes of CLEF 2013 (Cross Language Evaluation Forum) (2013

Medical image modality classification using discrete Bayesian Networks

In this paper we propose a complete pipeline for medical image modality classification focused on the application of discrete Bayesian network classifiers. Modality refers to the categorization of biomedical images from the literature according to a previously defined set of image types, such as X-ray, graph or gene sequence. We describe an extensive pipeline starting with feature extraction from images, data combination, pre-processing and a range of different classification techniques and models. We study the expressive power of several image descriptors along with supervised discretization and feature selection to show the performance of discrete Bayesian networks compared to the usual deterministic classifiers used in image classification. We perform an exhaustive experimentation by using the ImageCLEFmed 2013 collection. This problem presents a high number of classes so we propose several hierarchical approaches. In a first set of experiments we evaluate a wide range of parameters for our pipeline along with several classification models. Finally, we perform a comparison by setting up the competition environment between our selected approaches and the best ones of the original competition. Results show that the Bayesian Network classifiers obtain very competitive results. Furthermore, the proposed approach is stable and it can be applied to other problems that present inherent hierarchical structures of classes

MLM: A Benchmark Dataset for Multitask Learning with Multiple Languages and Modalities

In this paper, we introduce the MLM (Multiple Languages and Modalities) dataset - a new resource to train and evaluate multitask systems on samples in multiple modalities and three languages. The generation process and inclusion of semantic data provide a resource that further tests the ability for multitask systems to learn relationships between entities. The dataset is designed for researchers and developers who build applications that perform multiple tasks on data encountered on the web and in digital archives. A second version of MLM provides a geo-representative subset of the data with weighted samples for countries of the European Union. We demonstrate the value of the resource in developing novel applications in the digital humanities with a motivating use case and specify a benchmark set of tasks to retrieve modalities and locate entities in the dataset. Evaluation of baseline multitask and single task systems on the full and geo-representative versions of MLM demonstrate the challenges of generalising on diverse data. In addition to the digital humanities, we expect the resource to contribute to research in multimodal representation learning, location estimation, and scene understanding